The TimeLord's Daughter
by madladypoet
Summary: Our favorite TimeLord discovers that he has a daughter and sets out to find her. Yet old enemies of the Doctor have resurfaced seeking their revenge. Donna/Martha/Captain Jack/Face of Boe make appearances
1. Chapter 1

Prologue

_Prologue_

_Tardis_

_Somewhere in Space and Time_

The Doctor sat in front of the controls of the Tardis, staring straight ahead. Alone once again, the Doctor had no idea where to go and did not care. It seemed that he was destined to continue his existence alone. Oh, he had companions, but they were human, frail and eventually destined to leave him. He longed for a companion of his own blood.

But the last great time war had wiped them out. The Doctor remembered standing at the door of the Tardis and watching his home planet burn. The burnt orange sky was deep red as flames consumed everything living. He had tried to get back in time to save his wife, daughter and friends, but they were all gone.

For years afterward, the Doctor wandered simply existing until he met his first companion, Asha. She reminded him of his beloved deceased wife. The Doctor and Asha spent several months together, and the Doctor even considering becoming human to stay with her. Yet an upsurge of the Dalek had forced him to leave her and to keep her safe he never returned. That pattern would continue for the next thirty years--find a companion, show her the universe and leave her when it became too dangerous. Asha, Sarah Jane, Rose, Martha and Donna had all been the Doctor's companions and he had lost all of them. Eventually, he came to expect it, but he never got use to it.

"I am always alone" thought the Doctor, staring into the empty spaces around him.

_Beep, Beep, Beep, Beep_

Coming back to the present, the Doctor saw that he had an incoming transmission. Hitting the enter button on his keyboard, the Doctor reeled back in shock—It was the face of Boe. For a moment, his heart swelled with joy. The Doctor was thrilled to see that big old face.

"Boe." he cried out, genuinely overjoyed. "How can it be?!"

The last time the Doctor saw his old friend, the Face of Boe had given his life to save millions trapped in the undercity of New New York. The Doctor was always grateful to Boe for saving Martha since it was the Doctor's fault that she was nearly killed. He later learned that the Face of Boe was his old friend, Captain Jack Harkness. Thanks to Rose, Captain Jack became immortal and through the centuries his form evolved. It is ironic, the Doctor thought looking into the Face of Boe, that Captain Jack Harkness would evolve into the thing he always valued most: his face.

The powers of the universe, the Doctor thought, had a great sense of humor.

"My old friend," said the Face of Boe, "I can only evolve; I can never die."

"So what is your latest evolution?" asked the Doctor with a cheeky grin.

"Something called Cyberspace" replied Boe. "I can transmit to any computer through it."

For a moment, the computer screen crackled and lost focus. The Doctor felt his hearts literally stop at the loss of contact, but Boe soon came back into focus.

"I've been looking everywhere for you, Doctor." Said Boe.

"Really?" asked the Doctor in surprise. "Why me?"

"She needs you." replied the Face of Boe.

The pronoun she immediately caught the Doctor's attention. "Is it Rose?" he asked.

"No." replied the Face of Boe. "she is doing quite well.

The Doctor had to admit to himself that bit of news stung. Of all his companions since Asha, he had been the most emotionally attached to Rose. Losing her had been painful and not even the love of Martha or the affectionate companionship of Donna had completely dulled the ache of that loss. Yet, she had returned to him in a different form and although there were hints of the old Rose, she had become a different person.

The Doctor supposed everyone changed at one point or another.

Still, the Face of Boe had not given him the name of the woman who needed his help. The Doctor knew it had to be a former companion, so he began to reel off a list of names.

"Asha?" asked the Doctor.

"No." said the Face of Boe. "She is dead."

Again, the Doctor felt his hearts stop beating. Asha was dead. He had nearly become human for her and she was gone. He remembered their last meeting. The Daleks were set to invade earth and the Doctor knew he was the only one who could defeat them. Asha had begged him not to leave, saying that there was something important he needed to know, but he had left her without a backwards glance and had never returned. He always told himself it was to keep her safe, but he also knew that it was to keep himself from losing someone else he loved.

"Sarah Jane?" asked the Doctor.

"No." said the Face of Boe. "She is a mother now."

The Doctor was thrilled to hear that. Sarah Jane was a wonderful companion and although he had not loved her in return, he admired her and missed her companionship for many years after she was gone. He was glad to hear that she was a mother. He always knew that she would be smashingly good at being a mother.

"Martha?" asked the Doctor.

"No." said the Face of Boe. "She is a doctor and engaged to be married."

The Doctor again found himself thrilled to hear that another companion had found happiness. He had wanted to return Martha's love, but could not let go of the memory of Rose. Still, the Doctor knew that he owed Martha so much. She had saved his life countless times, all she got in return was unrequited love and her family destroyed. The Doctor was not surprised when she left him. In some ways, he felt that he deserved it. The Doctor could only hope to pay her back one day.

But right now, he was anxious to find out the woman's name.

"Well," he demanded rather loudly. "Who is she?"

"Her name is Emily." said the Face of Boe. "She has been looking for you these many long years."

The Doctor felt puzzled. His mind shifted through 900 years of memories, but he could not find a single recollection of a woman named Emily.

The Face of Boe shifted and appeared to be staring directly at the Doctor. "Emily is your daughter."

The Doctor froze. "That is not possible."

"Doctor" began the Face of Boe.

"My daughter is dead." replied the Doctor with a little more bite than he intended. The Doctor swallowed hard and remembered his little girl. She was the light of his life. She loved hearing stories of her father's travels. Every time, the Doctor returned home; his daughter would curl up in his arms as he recounted stories of his adventures. He had planned to train her to be a timelord when she grew up. The Doctor felt his jaw tighten at the memory. Staring into the screen, the Doctor felt himself get angry at the Face of Boe. His promises of companionship to the Doctor were beginning to fray on the Doctor's nerves.

"Why do you do this to me?" demanded the Doctor.

"Doctor . . ." began the Face of Boe.

"No." the Doctor thundered. "No more."

"Doctor" responded Boe. "Her mother is Asha."

The Doctor's mouth dropped open. Asha had been pregnant when he abandoned her. He had left behind his child and her mother. Guilt and shame washed over him. That was why Asha had begged him not to leave her, but left her he had as his obsession with destroying the Daleks stronger than ever.

"Doctor" said the Face of Boe. "She needs you." "They are coming for her."

"Who?" demanded the Doctor. "Who is coming for my daughter?"

"Everyone." Said the Face of Boe. "Your enemies cannot defeat you, so they will go after her."

The Doctor remained silent for a moment, then asked, "How did they know about her?"

"She is looking for you." responded the Face of Boe.

The Doctor set his jaw. "Where can I find her?"


	2. Chapter 2

Mansfield Road

_Mansfield Road_

_Outside of Harris Manchester College_

_University of Oxford_

_Oxford, England_

_9:30 a.m._

Emily Smith exited her college and walked quickly down the street and turn onto South Parks Road toward the examination school. This was her first year as a tutor and although she only had three students; she had an intense desire to see them succeed. Theoretical physics was a difficult field to succeed in even for the brightest of students and Emily's success made her a star in the field at the relatively young age of 29. She graduated from high school at the age of 15, attended Oxford taking a double first in physics and chemistry by the age of 18. Then Emily moved to Harvard University to complete her master's degree and return to Oxford for her doctorate. She spent two years at the John Hopkins University working as a research scientist until boredom made her seek out Oxford again. Luckily a post for a tutor in physics was open and with her credentials, Emily was a shoo-in for the position.

Her heels tapping on the cobblestone streets; Emily knew that it was more than luck that brought her to Oxford. It was fate. During the two years she spent in Maryland, her mother was diagnosed with cancer. Making trips back and forth between Baltimore and her mother's house in the Uffington had been difficult and exhausting, but ultimately rewarding. Not only did Emily get to spend these last days with her mother, she also found out some news about her father.

Unlike her schoolmates, Emily grew up not knowing her father at all. There were no pictures of him, her mother rarely spoke of him and Emily had to admit that she did not even know his name. Yet as Emily began to accelerate through her academic career, her mother often murmured that Emily got all of her talent from 'her father.' Still, he remained, to Emily, a mysterious figure; a man who lurked on the shadows of her small family. Growing up, Emily rarely gave much thought to the man she felt had abandoned her, but she knew that her mother was obsessed with him. Asha had never dated anyone since Emily's father left and Emily often caught her mother staring into the sky, whispering as if she was waiting for someone to return. Emily often found herself angry with her mother for wasting her life on some unknown man.

Turning her head, Emily watched as students, having completed their exams ran for the door. Looking through the crowd, she found her three students, George, Frank and Sherri. She had worked with them until two in the morning when she was too exhausted to carry on and had walked home. Young and with a fresh supply of Red Bull, the trio continued their studying until dawn. Emily had warned them that they needed sleep prior to an exam. Of course, they did not listen. Dragging themselves toward her, George, Frank and Sherri moved more like zombies instead of soon-to-be college graduates.

"Well?" asked Emily.

Frank and George both hugged her without saying a word and shambled on. Sherri looked at Emily and burst into tears. Emily hugged her student without saying a word and as she looked over her shoulder, she saw a man staring at her intently. He was tall, slender with dark brown hair and brown eyes. There was something familiar about him, although Emily could swear that they had never met before. Pulling away from Sherri's hug, Emily handed her pupil a pack of tissues and listened as the girl told her tutor how badly she had messed up her exam and how she was never going to graduate. Only half listening, Emily looked over the girl's shoulder at the strange man. He smiled at her and Emily felt a blush creep into her face. Was this man flirting with her? Normally, she would be thrilled since he was quite handsome, but something about it felt wrong. Turning her attention to Sherri, Emily saw that her student had calmed down and she urged Sherri to go home and get some sleep. Turning back, Emily saw the man was gone. Now free to look for him, she walked through the entire building but he was nowhere to be found.

Opening the front door, Emily walked outside and scanned the street, but the stranger was lost to her. Emily shuddered. The whole situation felt unsettling. She had a feeling that she was going to see that man again. Soon.

_7:00 p.m._

_Dining Hall_

_Harris Manchester College_

Emily Smith was neatly dressed in her favorite black dress and heels as she walked to the dining hall. While formal dress was required for faculty dinner, the steward rarely enforced it. Still, Emily had an overwhelming feeling that she needed to look her best for tonight's dinner. She thought about the man with brown eyes and wondered why he felt so familiar to her. His presence was unsettling and she had difficulty concentrating on anything else all day. Who was he? Why was he staring at her? What did he want?

Still, she was pleased to be informed by the department head that her students—Frank, George, and Sherri—had passed all of their exams with superior marks. Emily had run to the nearest pub, the White Horse, where she knew they would be holed up, to inform them. Frank ordered ale for everyone to the loud cheers of the bar patrons; Sherri burst into tears and ran outside to call her family with the good news and George grabbed Emily and planted a kiss on her that was so deep Emily could still feel the pressure of his lips against hers even now. She should have been embarrassed, but she was so thrilled to have her first three students succeed that she did not mind at all.

Standing outside of the dining hall, Emily tapped her lips and found her thoughts wandering again to the brown-eyed man. She shook her head. Why was she so obsessed with thinking about this man? Ever since her husband disappeared, Emily had rarely looked at any man sideways. The loss of Jack had been too difficult and the idea of dating again made Emily feel like she was replacing him. Emily had to smile to herself; she had indeed become her mother.

And at that moment, she missed her mother terribly. She wished that her mother had had a happier life instead of pining away for the man who had deserted them both. Still, Emily returned to Oxford with a mission of her own--to find her father.

Climbing the stairs, Emily opened the heavy wooden door and walked into the dining hall. Unlike most Oxford colleges, the dining hall at Harris Manchester was rather small. It was sparsely decorated and contained three long wooden tables for dining. The steward was directing the servers and the dining hall was full of loud, rambunctious conversation. Scholars, who spend the entire day teaching and reading, spend their entire evenings debating and fighting. Although Emily always enjoyed good conversation, tonight she wanted to dine and go home. Finding a spot at the end of one of the tables, Emily sat down. Lucky for her, the other scholars were engaged in deep conversation and her presence had gone unnoticed. Grabbing her napkin, Emily placed it on her lap and sipped some water when she turned to her right. Startled, she nearly jumped out of her seat. It was the man with the brown eyes again. His eyes were gleaming brightly and he seemed overly excited about seeing her again. Once more, Emily felt unsettled on the sight of him. He seemed harmless enough, but why was he so interested in her?

"Hello!" said the man, who sounded positively bubbly.

"Hello." returned Emily quietly, wondering if she should call for the steward.

"I'm the Doctor." said the man.

"Dr. Emily Smith." responded Emily. "You said the Doctor. Doctor of what?"

"Just the Doctor" said the man, happily buttering a piece of bread.

Emily felt annoyed with him. She didn't like being stalked and what kind of name was the Doctor anyway?

"Well" said Emily. "What do you want from me?"

The Doctor, as he called himself, looked amused. "What makes you think I want anything from you?"

Emily began to answer, but realized that he was right. She did not know this man and was being overly aggressive against someone she didn't know. Her mother would be appalled. Looking at the man, Emily felt strangely connected to him, but she didn't know why.

"I must apologize for my rudeness." said Emily. "I got very little sleep last night."

The Doctor didn't seem offended in the least. "No problem." "I understand you're the best in your field—theoretical physics, is it?"

Emily felt her body relax. While she was not up for academic conversation, she was thrilled that the conversation was steered in a safe direction. For the next hour, she explained her work in theoretical physics, particularly her specialty of predicting the changes of physical phenomena as the result of alien contact. The Doctor said very little, occasionally nodding, but focusing on her as if he recognized her from some past life.

Without warning, as she was going into detail about the impact of time events on physical phenomena, the Doctor leaned over and touched her on the face. For a moment, Emily felt the warm of his hand and saw a flash of her mother. Asha was in some sort of alien place and she was laughing as the room was spinning round. There was a man shouting something and running around the control area at full speed. Emily had never seen her mother so happy and the image of it almost hurt. As quickly as the image came, it was gone and Emily found herself hyperventilating. The Doctor had gotten her water and was holding the glass as she took sips of it. Emily felt her entire body shaking and tears running down her face. The Doctor signaled the steward and told him to take Emily home. As she walked out of the dining room, Emily looked back and saw the Doctor still staring at her with an expression of overwhelming sadness on his face.

At home, Emily took a long shower hoping it would wash away her pain and exhaustion. Climbing into bed, she dreamt of the spinning alien room and instead of her mother and the phantom man; Emily saw herself and the Doctor and they were both laughing as the room spun them toward their next destination.


	3. Chapter 3

Three days later

_Three days later_

_The Unit_

_New Hope Hospital_

_London, England_

Martha Jones carefully placed the tissue sample on the slide and slid it under the microscope. Since she began working for the Unit, she began cataloging the different alien species that were living on Earth. Martha was hoping to be done early, so she could get home to her fiancée. It was only three weeks to their wedding and Martha couldn't wait to get married. Simon was the perfect man for her. He was kind, loved her family and was a doctor himself. Best of all, he loved her in return. Martha had promised herself that she would never get into another relationship where she was pining after someone.

Even if that someone turned out to be as fascinating as the Doctor.

Martha smiled to herself as she remembered the Doctor and their time together. Although he did not love her in return and even had blamed himself for the destruction of her family, Martha still thought he was one of the most fascinating people/aliens that she had ever met. It was through the Doctor that so many amazing things happened to her. She met Shakespeare who wrote a sonnet about her; went to New New York and even to the end of time where she met another Timelord and the irrepressible Jack Harkness. Her parents got back together. Her brother, Leo, went into the service and her sister, Tish, had returned to school and was working on her law degree. Martha herself find her passionate calling in working with the Unit and using her medical skills to fight against aliens. Even better, Simon had come into her life and Martha knew that she would have never met him if he had not been for the Doctor.

Overall, Martha felt as though she owed the Doctor a great deal.

Concentrating on the slide, Martha did not notice as a man stood in her doorway and watched her work. Stepping back from the microscope, Martha stood up and turned to the doorway when she saw him.

"Doctor!" she cried out and ran toward him clasping him in a huge embrace.

The Doctor wrapped his arms around Martha and hugged her back as fiercely. Martha had been a great companion and he had missed her quite terribly when she was gone. Letting go of the Doctor, Martha gave him a once over. She smiled and shook her head.

"You never change do you?" she asked.

The Doctor smiled back. "You, Ms. Jones, have changed a great deal."

Martha took that challenge and put her hands on her hips. "Good or bad?" she asked.

"Actually," said the Doctor. "You look quite beautiful."

Martha grinned at him cheekily. "Why thank you." Cocking her head, she looked at the Doctor, "What brings you to this time and place?"

"Martha," the Doctor began, "I need your help."

"Anything," said Martha grabbing her stool and pulling it beneath her. "What do you need?"

The Doctor looked at her for a moment, sighed and pulled two handkerchiefs from his pocket. Hesitating, he held them close to his chest and then handed them to Martha. She cupped them in her hands delicately as if she could already sense their tremendous importance to the Doctor. Martha put them down on a metal tray and walked over to the sink to scrub up. As she did so, she asked the Doctor, "What are they?"

"DNA samples." replied the Doctor quietly.

"What species?" asked Martha, drying her hands.

The Doctor looked surprised. "What do you mean, what species?"

"Well," said Martha putting gloves on, "I know this has to be alien, so what species is it?"

Pointing to her computer, Martha told the Doctor, "I have been cataloging alien species for the Unit." "So far," she said, "I have managed to catalog over 1000 species."

The Doctor smiled. "Impressive work, Ms. Jones." "Now, you just have 990,000 more to go."

Martha's grin faltered slightly at the thought of all that work, but she managed to keep a brave front nonetheless. That, the Doctor admitted to himself, is what he admired about Martha. Her resourcefulness was great even in the face of insurmountable odds. The Doctor knew that he was alive because of that. After Rose, the Doctor had been reckless and Martha had been the person, for at least a time, to reel him in.

"So," said Martha pointing to the handkerchiefs lying in the tray. "What am I taking DNA samples of?"

"Me" said the Doctor. "And my daughter."

Surprisingly, Martha seemed nonplussed at the news the Doctor had a daughter. She merely nodded at the information and picked up the first handkerchief and several long strands of jet black hair fell out. The Doctor felt his throat tighten. It was Emily Smith's hair, and the Doctor was certain that she was his daughter. Martha unraveled the second handkerchief and it contained several short brown hairs. The Doctor snipped out some of his own hair for comparison.

Martha looked at the hairs for a moment and then up at the Doctor. He saw a great deal of compassion in her face. She knew how desperate he was for one of his own kind.

"Doctor," she began quietly. "How do you know this woman is your daughter?"

"The Face of Boe" said the Doctor.

Martha seemed surprised. "The Face of Boe is dead."

"No!" said the Doctor cheerily. "He's alive in cyberspace."

Martha smiled. "And the Face of Boe told you that you had a daughter."

"Yes." said the Doctor. "He told me where to find her."

Martha put the samples on a metal tray and picked up two tubes. "Who is her mother?"

The Doctor's cheery disposition faded. "Asha" he began, hesitated and then continued. "The Daleks came and I left her." Martha looked up at him. The Doctor was staring straight ahead. "I never went back."

"So she was pregnant when you left her?" said Martha.

"I think so." replied the Doctor "I don't know for sure."

"Hence the DNA test." said Martha.

"Yes." replied the Doctor.

Martha looked at the Doctor for a moment and then down at the samples. She seem to want to say something, but could not find the words. Finally, she looked up at the Doctor.

"Give me about 24 hours" said Martha. "I'll call you with the results." "Do you still have your phone?"

The Doctor tapped his breast pocket. "Always."

Martha smiled. "Have a good night Doctor."

"You too." said the Doctor. He turned to leave and then paused. "Martha?"

"I'm sorry." Said the Doctor.

Martha looked puzzled. "For what?" she asked.

"For destroying your family." said the Doctor. "For what happened between us."

Martha was stunned by the admission. The Doctor was not one for sentimentality. He must be really vulnerable right now, thought Martha. She smiled at the Doctor.

"Honestly," said Martha. "I owe you a thank you." "I wouldn't have the life I have now without you."

"Martha" began the Doctor. But Martha held up a restraining hand.

"Listen." said Martha. "My parents are back together and happier than ever. Leo and Tish have grown up and gone their own way. I have a great job and an amazing fiancée." She smiled at the Doctor. "That happened because of you."

The Doctor felt emotion well up in him. He knew that Martha saw his vulnerability and was being kind, but he also sensed truth behind her words. The Doctor couldn't find the words to express his gratitude to Martha, so he just hugged her instead. After a moment, he let her go and she smiled at him.

"Go on." Said Martha. "Get some rest and I'll call you tomorrow."

"Will do, Dr. Jones." replied the Doctor. "Will do."


	4. Chapter 4

Living Quarters

_Living Quarters_

_Harris Manchester College_

_5:45 a.m._

Emily Smith sat on the edge of her bed, holding her head in both hands. For the past four days, she had barely been functional. The extreme highs and lows she experienced reminded her of her mother who had been diagnosed with bipolar disorder when Emily was 12. Emily thought of herself as a rationale person, but for the past week, she had been teetering on the edge of a nervous breakdown unable to control her emotions from moment to moment. One moment, Emily was on a high, moving at such a frenetic pace that everything was a blur. The next moment, she would crash and find herself sitting on the floor with her eyes closed as painful memories surged—her mother's death, her husband's desertion, her lost baby.

There were other memories, too; memories which did not belong to her. Memories of a planet, not Earth, on fire. Its burnt orange sky glowing red and the screams of millions as the planet decayed into ash. She felt the pain and heartache of one lost amongst the stars. This memory could only belong to one person—The Doctor. Emily had not seen or spoken to him since that night at the dining hall. Yet, she knew that her erratic behavior and these strange memories were the result of her interaction with him.

Standing up, a wave of dizziness overcame her so strongly that she had to sit back down. Emily's fists curled up as she felt her anger mount. This was the Doctor's fault. Before meeting him, she had been a strong, resolute woman determined to live life on her own terms. Now, she was a tottering wreck, barely able to leave her apartment. To Emily, this was unacceptable. Forcing herself to stand, she walked to the bathroom and turned on the faucet. As she did so, she noticed daylight was beginning to crest on the horizon. Normally, Emily would already be outside completing her morning run. Now, she could barely walk to the bathroom. Bending over the sink, Emily splashed cold water on her face. She knew that somewhere in Oxford was the Doctor and she was determined to find him. Walking back into her bedroom, Emily got dressed. Sunlight was beginning to fill the sky. Last night's weather report promised that today would be sunny, balmy 65 degrees. The perfect weather, thought Emily, to find the Doctor. Today, Emily thought she would find answers to everything, including her past.

_Bodleian Library_

_Broad Street_

_8:27 a.m._

The Doctor stood outside the brocaded doors of the Bodleian Library waiting for it to open. Never a patient man, he thought about using his sonic screwdriver to open it. The Doctor pulled out his favorite tool and suddenly, he stopped, remembering what happened the last time, he entered the library without permission. A very angry librarian chased him out, chastising him for entering the library before it opened. The Doctor tried to explain that he had been there when Thomas Bodley first opened the library in 1602, but he was met with the door firmly being shut in his face. The Doctor laughed inwardly at the memory and it relieved some of his tension. Leaning against the door, the Doctor felt all of his 903 years weighing on him. He stared down the length of Broad Street wondering if Emily was looking for him. When he touched her face, the Doctor absorbed her memories and found most of them to be stark and painful. She had suffered so much loss at such a young age-the death of her mother, the disappearance of her husband and the loss of her baby. The Doctor knew that she was his daughter from her memories and her resemblance to her mother. Yet he needed a DNA test to investigate his theory. If Emily was indeed his daughter, then she shared at least half of his DNA. From what he learned about her, she was an exceptional scholar. Her climb through the academic ranks was nothing short of miraculous and her publications on time and space theory rivaled anything he had read on earth and that is what worried him. The Doctor knew that he was not the only alien in the universe who kept watch over the scientific discoveries made by humans. He had not been there when she was growing up, but now he needed to protect her from danger.

The Doctor turned as he heard the clicking noises of the screws in the door lock turning over. The same librarian, who had kicked the Doctor out years before, opened the door.

"Hello!" cried the Doctor. "It's been a while."

The librarian, whose name was Ms. Clennell, looked up at the Doctor and rolled her eyes. "Well" she said with an exaggerated sigh, "at least you waited this time." Turning her back on any further conversation, the librarian walked back into the building with the Doctor following. Ms. Clennell, obviously irritated by the Doctor's presence, proceeded to ignore him as she walked back to her desk. The Doctor usually left people alone, but he needed information about his daughter and he believed that this woman would know her.

"Erm" asked the Doctor clearing his throat "Do you know Emily Smith?"

The librarian turned around and pierced him with a glance. "You mean Dr. Emily Smith?"

"Yes!" said the Doctor with some relief. "What do you know of her?"

"Smart, talented, nice" barked Ms. Clennell. She stopped walking and turned to stare at the Doctor. "She obeys the rules."

The Doctor grinned at the jab. "Does she come here often?" asked the Doctor.

The librarian walked up behind her desk and sat down. From there, Ms. Clennell could stare down at the Doctor and the look was not too pleasant. Staring at him over her glasses, the librarian found that she did not like this man. She knew every tutor and lecturer at Oxford and she was particularly found of Emily Smith, having known her since the girl arrived here at Oxford as a fifteen-year-old prodigy. Ms. Clennell remembered the girl staying at the library for hours at a time, in part, to escape classmates who seemed to take pleasure in bullying her. She had heard about Emily's collapse at Harris Manchester College dining room and the man accused of causing it fit the Doctor's description perfectly. Leaning on the desk, Ms. Cannell wanted to make sure that her choice of words was clear to this man.

"Dr. Smith" she began in an even tone. "often comes in here to work."

"Oh great" said the Doctor. "If I could just find out when . . ."

"Why?" asked Ms. Cannell, her voice growing colder. "So you can cause her to collapse again?"

The Doctor's eyes grew wide. He had forgotten that Oxford, despite its international reputation, was in fact a small college town. Someone with Emily's reputation, he reckoned, would make her the center of attention here. Her collapse at dinner, the Doctor remembered, would probably be the talk of the school.

"Well" said the Doctor. "I just wanted to check up on her."

"Do you know" snapped Ms. Cannell "that she has been acting erratically ever since?"

"Well, I" began the Doctor.

"There is no 'I' Doctor" retorted the librarian. "This is not about you." She sighed for a moment, then shook her head. "This is about a young woman that many of us care about."

The Doctor stood for a moment and said nothing. As badly as he wanted his daughter in his life, he also realized that dragging her into his world might cause her even more pain. He didn't want that. Looking up at Ms. Cannell, he nodded that he understood and turned to go. As he was walking out of the library, his cell phone buzzed. Grabbing it from his coat, he saw that it was Martha. Flipping it open, he quietly said hello.

"Doctor" said Martha "I've got your DNA results."

"She's my daughter" said the Doctor without feeling.

"Yes" said Martha. "The match between your DNA and hers is 100."

"Thanks Martha" said the Doctor. He started to hang up when Martha shouted into the phone.

"Doctor!" yelled Martha. "Don't hang up!"

The Doctor put the phone to his ear. "Yes" he said quietly.

"The DNA match is positive" said Martha. "But most of her genetic makeup is human."

The Doctor stopped walking and stood just outside of the library. Chewing on his lip, the Doctor's brain went over a million calculations of what this might mean for his daughter. The conclusion was too painful for him to comprehend.

"This means" said the Doctor "that she will die."

"Yes" said Martha quietly. "Her DNA does not show that she has any of your regenerative powers."

"That explains it" said the Doctor.

"Explains what?" asked Martha.

"Explains why she has been having a reaction to the memories I passed on to her" said the Doctor.

"Doctor" said Martha "You cannot pass your powers to her." The Doctor could hear the click of keyboard buttons as Martha was typing. "In fact" said Martha. "It might be best if you did not have any contact with her at all."

"But" replied the Doctor quietly "I need her."

"I know" said Martha, "and you are wonderful." The Doctor could hear that Martha had stopped typing and was putting all of her energy into the conversation. "But you are fire and ice" whispered Martha "and sometimes those who love you pay a price for it."

The Doctor felt himself grow cold. Martha and Ms. Cannell were right. He needed to leave his daughter alone. Closing his eyes, the Doctor searched his mind and found her memories. Despite the bleakness she had faced, Emily had always found happiness in her every day life--whether it was working with her students, laughing with her colleagues at the pub, or walking the countryside near her grandfather's house in Uffington. She had faced loss, like her father, but unlike him, she tried to put down roots and invest in those around her. She deserves to live her life, thought the Doctor, without the constant danger he would put her in.

"Doctor" asked Martha. "Are you there?"

"Yeah" said the Doctor. "Thanks Martha, I'll speak to you soon." Without another word, he hung up and began walking aimlessly down Broad Street. The Doctor cut across Cornmarket Street to High Street and headed for the Botanic Gardens where he left the Tardis. Walking past the examination schools where he first saw her, the Doctor was stopped by a voice.

"Oi" shouted the woman, causing the Doctor to turn around. It was Emily. She marched straight up to the Doctor until they were face-to-face and he could have sworn that she was ready to punch him. Standing this close to her, the Doctor could see that her eyes were red with dark circles underneath them. My memories, he thought, have been too much for her.

"I'm sorry" he said quietly and turned to go. Emily grabbed him by the arm and shook her head. "We need to talk."


	5. Chapter 5

_The White Horse Pub_

_Broad Street_

_10:30 a.m._

The Doctor and Emily found a table near the window. The pub offered an excellent view of the Bodleian Library and for the Doctor, the scene provided a welcome respite from the angry face of his daughter. He remembered convincing Thomas Bodley to create a library at Oxford and standing there when the first books were brought in.

Ah, thought the Doctor, that was a fine day.

The waitress brought over their drinks and the Doctor sipped on his ale. Normally, he avoided alcoholic drinks, but this situation seemed to call for it. Emily was sticking to tea and like her father, she was staring out the window. She let out a sigh and turned to face him. Both father and daughter gave each other half smiles, but neither one was willing to start the conversation. Finally, Emily sighed and looked over at her father.

"You're my father" she said quietly.

"Yes" said the Doctor equally quiet. "I had a DNA test completed to confirm it."

Emily looked confused. "A DNA test?"

"Yeah" said the Doctor suddenly felt uncomfortable and began stammering. "The night at the Harris Manchester dining hall . . . Remember you became ill when I touched you. . .Well, I also took a snippet of your hair."

Emily stood up, knocking over their drinks. She placed both hands on the table and bent down to stare the Doctor squarely in the face. "You stole my hair?" she hissed.

The Doctor backed away from his daughter's angry face. He spread his hands in an effort to be civil. "I had to be sure."

For a moment, there appeared to be a stand-off between father and daughter. Emily's entire body seemed to bristle with anger while the Doctor attempted to keep her calm. He leaned forward and looked quietly into his daughter's eyes.

"I know that you are angry" he said. "But you need to sit down so we can talk rationally."

Looking at him, Emily felt her anger defusing. She was angry at him for abandoning her and her mother, but in his eyes, she saw his pain at having done so. Sitting down, Emily felt tears slip from her eyes She had come to Oxford with the hopes of finding her father and now that she had she wanted to be far away from him. Reaching into her pocket, Emily felt the letters that her mother had given to her before she died. One letter was addressed to Emily and another was addressed to a person called the Doctor. In Emily's letter, her mother explained that the Doctor could be found at Oxford. After accepting her new post, Emily spent months looking into the records of every professor on staff at the University's different colleges, but none of them matched her mother's description of the man. Emily became convinced that she would never find him. Sighing, she pulled the letters out of her pocket and placed them on the table. She looked at the Doctor and quietly spoke.

"She described you differently" said Emily pushing the letters across to the Doctor.

"That's because I look differently from when she knew me" said the Doctor touching the letters with his fingertips. "I have the power to regenerate."

Emily looked thoughtful for a moment and the Doctor could see her mulling over numerous calculations in her head. He smiled at this and for a moment, the Doctor felt a true connection to another being. Emily looked up somewhat disconcerted.

"What ARE you looking at?" asked Emily with a slow smile spreading across her face.

"You" said the Doctor with a grin. "I'm looking at you."

"And?" asked Emily. "What do you see?"

"My daughter" replied the Doctor. "Someone quite wonderful."

Emily felt a slow blush cross her face. Biting her lip, Emily studied the Doctor for a moment. She tapped the letters with her finger.

"You need to read these" she said quietly. "They are from my mother."

The Doctor nodded and looked grim. He had been devastated by the destruction of his planet and the loss of his family, but in his grief, he had destroyed other lives. Picking up the letter, the Doctor felt the weight of his destructive path. He took the letter and held it to his letters. Inhaling, he could still smell the traces of Asha's perfume on them. He could remember the last time he saw her. How tightly her arms were wrapped around him and the tears that fell on the lapel of his brown coat. The day was so warm as it always was in Uffington during the spring. He remembered promising her that he would return, then getting in the Tardis and leaving. He could hear her voice as the Tardis vanished into time and space. He always thought he would return, but war left him a bruised and battered man and he felt that she deserved a better stronger man. Looking at his daughter, the Doctor realized that he had left behind a bruised and battered woman and child. Nodding at Emily, the Doctor opened the letter addressed to him. As he did so, Emily stood up. The Doctor looked at her in surprise.

"You're not staying?" he asked.

Emily shook her head. "I'm taking a walk." She put on her coat. "You need to read these on your own." With a careful nod, she turned and walked out the door. The Doctor watched her walk down Broad Street in the crisp morning air. She caught a rather dashing figure, thought the Doctor, like her father. Turning his attention back to the letter, the Doctor opened it and began reading.


	6. Chapter 6

_Three years earlier_

_10:45 a.m._

_Uffington, England_

My dearest Doctor:

I write this letter to you with my last breath. I was diagnosed with cancer about two years ago and after a brave fight, my time is coming to end. It is with this time left that I am writing to you about our daughter, Emily. She will need your help in dealing with what's to come.

Over the last twenty-six years, I have been monitoring alien sightings on earth, in part, to protect Emily. After you left, I went to Torchwood and told them about my child. Since then, Emily has been under the protection of Torchwood and Captain Jack Harkness. She is human, but has so much of your talent. When she was a child, she dazzled her professors with her abilities and frightened me with her precognition. Luckily, I was able to teach her to channel her abilities in science and she has become an amazing success. Still, I fear what will happen to her while I am gone.

Emily does not know her father's identity and is angry at being abandoned by him. Since the loss of her husband and child, that anger has intensified as well as her desire to find you. I have encouraged her to stay at Oxford with the hopes that some day you would return. Captain Jack has promised me that he would do what it takes to find you. I trust that he will keep good on that promise. She will now need your protection.

There has not been a day that has gone by where I have not thought of you. I knew on the day you left that you were never going to return. I wanted to tell you about your child, but I did not want you to feel obligated to stay. Know that I have always kept you in my heart and your daughter was safe within my care.

Before I began this letter, I went to look in on Emily. She was asleep and for a moment, she so resembled you that I thought, for a moment, that you had returned to me. She stirred for a moment and murmured some calculation and it reminded me of you. Emily has much strength, but her weakness has always been her compassion for others. She has always willing gone into danger and with the invasion to come, I fear that she will do something reckless.

As you know, the danger to earth is ever-increasing. Attacks by aliens are becoming the norm and Torchwood has evidence that proves that the Daleks are preparing to mount an attack on this time period on earth within the next four years. Emily will throw herself into danger to defend her family, friends and country. You will need to guide her through this.

That is all, my love. I hope this letter finds you and finds you well.

Love,

Asha

_The White Horse Pub_

_Broad Street_

_11:30 a.m._

The Doctor ordered another pint of ale. Normally, he avoided human alcohol since it made him ill, but after reading Asha's letter, he decided that another pint would be necessary. He knew that his daughter would be returning shortly and he needed to be ready to face her. Looking around the quiet of the pub, the Doctor realized that he was alone there except for the bar keep. In that moment, the Doctor let his tears fall. He was a man quick to anger and rarely cried, but this time he felt the need to. The Doctor spent his life trying to help others, specifically humans, stop from making the same mistakes he made and while he had saved millions of lives, he could not stop thinking about the lives he destroyed and the people he hurt. Asha deserved better from him. Lost in his own thoughts, the Doctor did not hear a patron enter the bar.

"Doctor?" asked a voice. " Is that you?"

Looking up, the Doctor inadvertently let out a groan. It was Captain Jack. While he did not dislike Jack, he did not consider Jack to be one of his favorite people either. Still, he needed to talk to Jack about his daughter and with a grand gesture, he indicated the seat across from him. Jack slid in the seat and indicated to the barkeep that he did not want anything. Jack looked across at the Doctor, who was staring at him with folded arms, and gave his friend a loop-sided grin.

"I've been looking everywhere for you." he said studying the Doctor's face "Have you been crying?"

The Doctor quickly wiped his eyes with his sleeve coat and glared at Jack who, in turn, looked amused.

"How did you find me?" asked the Doctor.

"Martha" said Jack. "She told me about your daughter." Jack grinned. "I was wondering what the daughter of the famous Doctor would look like."

The Doctor leaned forward on the table. "You flirt with my daughter and there is no telling what I will do to you." The Doctor let out a sigh. "Besides, you have already met her."

Jack looked surprised. "Who is she?"

With that, the Doctor pushed Asha's letter across to Jack who picked up gingerly and began reading. By the time he finished, Jack looked ill. He handed the letter back to the Doctor and looked around.

"Is she here?" he asked.

The Doctor looked at Jack somewhat perplexed by his friend's behavior. Jack was always so smooth even in the face of danger. Now he looked somewhat afraid.

"Yeah" said the Doctor. "She went for a walk." "She should be back soon."

"I'd better go." said Jack standing up. He paused for a moment as though he were uncertain of what to do next. Then he stopped and leaned in toward the Doctor. "Don't tell her that you ever saw me."

The Doctor felt confused. What was going on here? Why didn't Jack want to meet Emily?

"Jack?" came a small female voice from the doorway. "Is it really you?"

Both the Doctor and Jack turned to see Emily standing in the doorway. She looked shocked at seeing Jack. Then she promptly ran over and hugged him. At that moment, the truth dawned on the Doctor. Jack was his daughter's husband. Looking at Jack's face, the Doctor saw that Jack was crying. Letting go of Emily, Jack looked at her and kissed her passionately. Gently, he let her go and pushed her into the hands of her father.

"I have to go Emily" said Jack. He looked at the Doctor. "I'm sorry." Then, as Emily began calling out for him, Jack turned and ran out of the door. Emily tried to go after him, but was held back by her father. Then Emily turned and fell into her father's arms. The Doctor stood in the pub holding his daughter. At that moment, the Doctor's cell phone buzzed. Tenderly, the Doctor placed his weeping daughter in a chair and signaled for the barkeep to bring her some tea. Grabbing his phone, the Doctor opened it.

"Hullo" asked the Doctor.

"Doctor!" shouted a female voice. "Is that you?"

"Donna?" asked the Doctor. "Why are you shouting?"

"It's the Daleks!" shouted a female voice from the background. "They are back."

"Martha!" shouted the Doctor. "Tell me what's going on!"

"Doctor!" yelled Donna into the phone. "We need you."

Before the Doctor could respond, the line went dead. Looking down, he saw that Emily was staring up at him with a determination that he did not recognize. She still had tears rolling down her face, but she stood up and wiped them away. When she began speaking, her voice cracked but remained steady.

"What's happening?" she asked.

"An invasion in London." said the Doctor. "The invasion that your mother warned me about."

Emily nodded. "What do we do?"

The Doctor grabbed her arm and walked with her out the door. "Listen," he began. "I don't . . ."

"There is no don't" snapped Emily. "An invasion is happening in MY country and I want to be a part of the solution."

The Doctor appeared to be formulating a response, but Emily cut him off. "I'm sure that Mum told you about me, but this is still my decision." She pulled her father's hand off of her arm and stared at him defiantly. "I'll go to London with or without you."

The Doctor smiled and chuckled to himself. "You remind me so much of your mother."

"Come on" he said grabbing Emily's hand. "We are heading to my ship"

Emily ran with her father. "You have a ship?"


	7. Chapter 7

_Covent Gardens_

_London, England_

_11:32 a.m._

The TARDIS landed rather loudly in the Covent Garden Piazza. Emily and the Doctor emerged somewhat bruised with the Doctor muttering that the TARDIS was not to be used for flying. Emily grabbed her father's arm as they looked around.

"No one is here," whispered Emily as they cautiously looked around. "I've been to Covent Gardens many times and it is always full."

"Come on," said the Doctor. "Let's go find Martha and Donna."

"Where is New Hope Hospital?" asked Emily as they began leaving the Piazza.

"A few blocks west," said the Doctor. "Martha and Donna were working on something for me when the Daleks attacked."

"What were they working on?" asked Emily.

For a moment, the Doctor looked uneasy. "Just something," he muttered so quietly that Emily had to strain just to hear him.

"Anyway," said the Doctor changing the subject, "how long were you married to Captain Jack?"

"Four years," replied Emily with her voice breaking. "I thought we were so happy, then after the Maggie died, he left."

"How did your baby die?" asked the Doctor quietly.

"SIDS," said Emily. "We put her to sleep in her nursery and she was fine." Emily stopped and looked out at the Thames River. London was eerily quiet, which worried the Doctor who grabbed his daughter's arm to get her moving. "Jack went into the room the next morning to wake her up." Emily shook her head. "She was gone."

"I'm sorry" said the Doctor squeezing Emily's arm affectionately. "Then what happened?"

"After the funeral," said Emily, "Jack was not the same." Emily's body was shivering at the memory and the Doctor took off his coat and put it around her shoulders. "He spent hours at Torchwood going over Maggie's case." Emily pulled the coat around her shoulders tighter. "Then one night, I received a phone call from Torchwood—Jack was dead." Tears began to spill from her eyes. "I can not believe that it was all a lie."

"Well," began the Doctor, "he was trying to protect you."

Emily stopped and glared at her father. "You know," she snapped, "I am tired of people trying to protect me."

The Doctor opened his mouth to reply, but the look on Emily's face warned the Doctor that his opinion was not wanted. For the next two blocks, father and daughter walked along in silence before Emily spoke up.

"Who are these Daleks?" she asked.

"My greatest enemy," said the Doctor. "There was a war." "The last great timewar." The Doctor sighed. "My home, my planet were all destroyed."

"Did you have a family?" asked Emily.

"Yes," said the Doctor. "A wife and a daughter." The Doctor's voice went cold. "They both died."

"I'm sorry," said Emily. "When did you meet my mother?"

"A few years afterwards" said the Doctor with a smile. "She was so alive; she brought me back to life."

"Why did you leave her?" demanded Emily, who stopped walking and glared at her father.

"Because of them!" whispered the Doctor savagely, grabbing Emily and pulling her to the nearest building.

Hiding in the doorway, Emily and the Doctor looked at several machines fly by. The machines were about five feet tall and had a periscope that appeared to be the eye of the machine. The machines appeared to be scanning for something. The Doctor was gripping Emily so tightly that she winced under the pain of it.

"They always win," snapped the Doctor, "while I lose everything."

Emily looked at her father's determined face and felt some of her anger at him deflate. Although she had lost a great deal, he had lost even more—his family, his friends, and his planet.

"I'm sorry," said Emily.

The Doctor looked down at his daughter and smiled. "I'm sorry too." Then he turned and looked out. "It looks like they are gone; we'd better run for the hospital.

Holding hands, father and daughter ran for the hospital.


	8. Chapter 8

_The Unit_

_New Hope Hospital_

_London, England_

_11:45 a.m._

Donna Noble tried not to scream. She has come to the Unit about 6:00 a.m. to help Martha with a project for the Doctor. They had nearly completed their task when news reports immediately filtered in showing the Daleks attacking London. Donna did not recognize them, but Martha knew immediately what to do. She called for a lockdown, put the Unit, Torchwood and the special services on alert and kept Donna calm as the Daleks flew around destroying the nearby Covent Garden Piazza. Donna tried to get out to protect her family, especially after receiving a phone call from her beloved grandfather shouting that there was another attack before the line went dead. Donna became hysterical and it was only Martha's common sense that kept her calm.

For that alone, thought Donna, Martha deserved a medal.

Still, the thought of her grandfather out there, possibly dead made her want to scream and shout, but Donna knew that Martha was right. Screaming wasn't going to help her grandfather, only the Doctor could do that.

The two women had positioned themselves by the only entrance into the Unit. They waited for the Doctor and Emily to come in. The incoming news showed that the attack began in London and was quickly spreading throughout the country. Martha told Donna that she suspected that England was going to be cut off from other countries as the Daleks dug in for a world wide attack.

"Are you sure?" asked Donna.

Martha nodded grimly. "I've seen it happen before."

"What do we do?" asked Donna, not sure that she actually wanted an answer.

"The Unit, Torchwood, Special Services have all made plans for this type of encounter," said Martha.

"Why do I feel a 'but' coming on?" said Donna.

Martha sighed. "Honestly, we don't know if our plans will actually work." She reached into her jacket pocket and pulled out her cell phone. "That's why I have the Doctor on call."

The Doctor, thought Donna, it had been a while since she had seen him. She thought that she would travel with the Doctor forever, but instead returned home to the promise of a normal life with a husband and possibly children. After her disastrous first attempt at marriage, Donna spent time on earth reclaiming herself. When she ran into the Doctor, she found a way to make herself useful instead of being the useless Donna that only served to create trouble rather than solutions. Still, she realized that her time with the Doctor was better spent helping on earth.

That's why Donna created a temp agency.

As ludicrous as it sounded, a temp agency allowed Donna to place temps in some of the most important corporations and government agencies in Britain. Donna worked with Martha and Torchwood to train the temps to be on the lookout for any type of alien invasion. So far, Donna had been successful in helping Torchwood and her country discover and control alien life in Britain.

Donna's mother had never been more proud of her daughter.

Still, Donna had not been prepared for an invasion of this type. These Daleks, whatever they were, were only interested in destroying mankind. Donna gripped her weapon tightly. Her granddad was out there and God only knew if he was okay. Donna felt tears begin to slip. Her granddad was the only person who ever really cared about her. To lose him was inconceivable. Donna was using money from her business to take care of her granddad and was convinced that he would live into an old age. But now he was out there with those things, thought Donna, and I have failed him.

"Donna?" asked Martha tentatively.

"Yea." replied Donna.

"Your granddad is going to be alright," said Martha. "He's a smart man and has dealt with aliens before."

"But these Daleks are a whole different breed!" exclaimed Donna.

"Yes," said Martha carefully measuring her tone, "But we are fully prepared to fight them." Reaching over, she squeezed Donna's shoulder. "If you want to see your granddad again, you are going to have to prepare yourself for battle."

Donna nodded and wiped her tears away with her shirt sleeve. She looked over at Martha and gave her friend a half smile. "Sorry," she said in a half whisper, "I always seem to lose it at the wrong moment."

"Don't worry about it," said Martha with a smile. "All of us go through that."

"Except the Doctor," said Donna with a sigh.

"Except the Doctor," replied Martha, "although with what we have found out, he may lose it."

"Why would he want to put her through that?" asked Donna.

"Eternity" said Martha. "The Doctor is looking to spend eternity with someone." Martha shrugged. "She's his daughter and as close a candidate as anyone."

"But you said that he swore that he would never . . ." began Donna.

"I know," Martha interrupted, "but look at it from his end, his family, his planet, everything he loved is destroyed." She breathed out a sigh and stared the length of the corridor. "Even his relationship with us, humans, is measured by time." She looked at Donna sadly and smiled. "We die and he cannot." Martha looked grim for a moment and then gave a short shrug. "I can understand it."

Donna nodded in agreement. "The question is will his daughter."

"Only time will tell," said Martha.

Neither woman spoke again until there was a banging on the door. Donna tensed while Martha stepped cautiously forward. "Oi!" she shouted, "Who is it?"

"Martha," shouted a male voice. "It's the Doctor!"

Martha ran forward and opened the door. The Doctor slipped in followed by a young woman. Both were out of breath after running. Martha and Donna ran up and hugged the Doctor while the young woman stared at them. Getting his breath, the Doctor introduced Martha and Donna to his daughter. "Ladies," he said between breaths, "this is my daughter, Emily Smith."

Emily walked forward and offered her hand. Donna noticed that her hands were shaking. She squeezed the young woman's hand and Emily smiled gratefully.

"So what's status?" asked the Doctor.

"We've lost contact with everyone" said Martha. "Torchwood, the Unit, Special Forces" Martha was shaking her head. "There's no one." "What's worse, it's quiet out there."

"My granddad," said Donna in a shaky voice, "he's out there."

"We'll find him Donna," said the Doctor. "I promise." He looked over at Martha. "I need access to your mainframe right now."

"Come on," said Martha and all four ran into the control room. The monitors outside of the Unit showed that the hospital was empty and the outside of the hospital was deserted. The Doctor shook his head. "That's weird." He grabbed the controller for the outside cameras and pan them 360 degrees. "No one is out there." "How can that be?"

"I don't know," said Martha. "There is something very wrong here."

"Does Torchwood have any plans in place?" asked the Doctor.

"Torchwood, the Unit, Special Services all have plans in place," said Martha. "But I have no idea where everyone is."

"I do" said Emily, speaking for the first time. "It's something that we have been working on at Oxford."

She looked at everyone. "We've been working on a space-time continuum in the case of an alien invasion. Everyone in Britain has been tagged with a special device in the case of an alien attack. The tag moves them into a parallel space-time." Emily looked at Donna, "So your grandfather is safe." Donna responded by bursting into tears.

"Why weren't we informed?" demanded Martha. "We deserved to know."

Emily shook her head. "This was incredibly top-secret." She sighed. "We weren't even sure that it would work."

"What a minute," said the Doctor. "How could you tag the entire country?"

"Inoculations against SARS," said Emily. "The government planted a story that SARS had been found in Britain and required that the entire country be inoculated."

"And instead you tagged the whole country" said Donna, looking at Emily admiringly. "Brilliant!"

Emily managed a half-smile but looked embarrassed. "Only key personnel were not tagged so they could stay here and fight." She looked around the control room. "That would be us."

"And me" said a male voice behind them. Everyone but Emily turned around. It was Captain Jack. "Come on" he said gesturing to them. "There is something you need to see in Torchwood."

Everyone but Emily moved out of the control room. Jack started to go to her, but a look from the Doctor warned him to stay away. Jack left the room and the Doctor went over to his daughter. "Emily?"

She turned and he could see that she was crying again. Hastily, she wiped her tears away and smiled at her father. "I can handle this, for the good of the country." Wrapping her arms around herself, she walked out of the control room followed by the Doctor.


	9. Chapter 9

_Torchwood_

_London, England_

_1:30 p.m._

Emily sat on the outskirts of the conversation as Jack, the Doctor and others discussed how to end the war the Daleks brought to Earth. As much as she wanted to participate, to be there to help her country, Emily could not bring herself to be in the same room as Jack. She kept her back to the group, but Donna could tell from the young woman's body language that she was listening. While the others were intent on their plans, Donna watched Emily struggle with her own feelings. Donna could understand that. In a world where time and space were not constant, relationships often failed at the whim of a specific event in time. Donna did not know all of the specifics of Emily and Jack's relationship, but she suspected that something happened to rip them apart. Donna hated it. As an incurable romantic, she always hoped that any couple would come together and stay together. It gave her hope for her own future. Stepping away from the conversation, Donna walked over to Emily and put her arm around the young woman.

"Come on," said Donna, "let's take a walk."

Donna and Emily walked away from the conversation. Emily's eyes were dry, but red and the pain was evident in them. Donna kept her arms around the young woman.

"Come on luv," said Donna, "tell me what's the story between you and Captain Jack."

Emily had no idea why, but she told her story to Donna. Her marriage to Jack, the loss of their daughter, his disappearance, and the fact that she thought he was dead. By the time she ended, Donna was in tears too. Breathing in, Donna looked at the younger woman.

"Look," she told Emily, "I know this is hard, but you have to put your personal feelings aside."

"I've tried," said Emily, "but it's all too much." "First, my dad shows up, then my not-so dead husband." Emily shuddered. "I always thought I was tough, but now I know that is not true." She paused and looked over at Jack and the Doctor. "I need to get out of here if I am going to help."

"Where would you go?" asked Donna.

"Glastonbury, "replied Emily. "That is where the tear in time and space is." "That is where we sent everyone through to a parallel world." She looked at Donna and crept closer. "I didn't tell the group, but there is an inherent danger in what we have done."

Donna suddenly felt her blood run cold. "What do you mean?"

Emily inhaled. "There is a possibility that we may not be able to bring people back." "They may end up stuck there." Seeing the shock on Donna's face, Emily turned away. "Others from that world may end up over here, and even the Daleks may end up going through the tear to other parallel worlds." Emily turned around and faced Donna. "That's why you probably should not have congratulated me on creating that world." Emily rubbed her face with her hands. "There are dangers in acting like God; just ask the Doctor."

Donna did not say anything and tried to absorb what she was being told. Everyone in Britain save for a few people were sent to a parallel universe, yet if the Daleks or the other worlds find this tear then this reality could be forever changed. She looked at Emily and saw how miserable the young woman was about playing 'God.' Donna put her hand on the young woman's shoulder and Emily looked up.

"Without a doubt, you are your father's daughter," said Donna, "You should be very proud of yourself."

"Why?" asked Emily numbly. "Instead of creating a solution, I may have created an even bigger problem."

"Many lives were saved because of you," said Donna, "You took a risk; someone had too." Donna nodded over to the Doctor. "Your dad would have done the same."

Emily looked over at the Doctor. "Dad," she said with some finality. "That word sounds so strange to me." Emily looked at Donna somewhat disconcerted. "He looks at me like I am the answer to his prayers."

"You are," said Donna. "He has been looking for a companion of his blood for some time."

"I'm human," said Emily, "I cannot be with him forever."

Donna felt herself hesitate. She wanted to be truthful with Emily. She felt the young woman deserved it. Yet Emily's fragile state of mind may not be able to take the truth. How would Emily deal with the fact that her own father might try to manipulate her DNA and take away the essence of what made her human? That is what she and Martha discovered for the Doctor. He wanted to know if Emily's DNA could be manipulated and through Martha's work at Torchwood they discovered that it could be. Upon that discovery, Martha and Donna knew that this would create a difficult situation for the Doctor. Could he forever force a change on a woman he barely knew? Was his desire for a lifelong companion so great that he would be willing to do so? Both Martha and Donna weren't sure they wanted to know that answer.

"Donna?" asked Emily. "Are you okay?"

"Yea, luv," said Donna. "I'm fine." "What are you going to do?"

"I'm going to Glastonbury," said Emily, pulling out her Blackberry.

"How are you going to get there?" Donna asked. "Glastonbury is a hundred miles from here."

Emily suddenly grinned. "You have your backup in the Doctor." She began scrolling down until she found the number she was looking for and punched it. "I have mine."

_Meanwhile_

The Doctor, Martha, and Jack were carefully gathered around a computer in Torchwood's central hub. Jack was bringing up videos cameras that Torchwood had placed in every major city in Britain. Each camera showed the same: every major British city was empty. Jack grinned. "You have to hand it to your daughter," he said looking up at the Doctor, "she's got skills."

The Doctor's calm demeanor suddenly looked stern. "You mean your wife?"

Jack's face changed as well. "You don't understand everything that happened." He glared at the Doctor. "What I did," he said, "I did it to protect her."

"You abandoned her" said the Doctor savagely. "You left her when she needed you the most."

Jack smiled at the Doctor. "You did the same to her mother." He leaned forward until he and the Doctor were nearly nose-to-nose. "So don't judge me."

"Guys," said Martha. "Can we have this mano-o-mano discussion later?" Martha stood up and put her arm between them separating them from each other. She looked from one to the other. "We have more important issues to deal with right now."

The Doctor and Jack backed away from each other. Martha knew that both men would have this conversation again. "Now," said the Doctor, "what about this tear?"

"What tear?" asked Martha.

"The tear Emily had to create in order to send most of Britain to a parallel universe" said the Doctor. "There is a chance that we might not be able to bring most of Britain back or even worse, other people from parallel universes could come here and the Daleks could move between worlds. "

"Great," said Martha. "Now what do we do?"

"Go to the source of the tear," said Jack. "bring our people back and close it forever."

"What about the Daleks?" asked Martha. "We can't exposure a general populace to the Daleks."

"We need to get rid of the Daleks first" said the Doctor. "I think I know a way to do that."

"Doctor," said Martha in a warning voice, "don't you dare!"

"Martha," said the Doctor, "I can lure them into space." The Doctor ran his fingers through his hair until it stood up. "It is the only way."

"Your wrong," said Jack, "They didn't come to Earth for you." He looked over at Emily who was in deep conversation with Donna. "They came for Emily."

"Why?" asked the Doctor. "What would they want with her?"

"Her abilities," said Martha, "she has your abilities, but she is still human."

"Which means they can control her" said Jack, "and even force her to change."

"Change into what?" demanded the Doctor, although his face showed that he already knew the answer.

"A dalek-human-time lord hybrid," said Martha, "I suspect they have been watching her for years, waiting for her to grow up."

"I wish they had waited for our daughter to grow up," said Jack with sadness, "They tried to take her when she was small, probably to get to us . . ." He paused unable to continue. "She died."

"The Daleks killed my granddaughter?" asked the Doctor.

"Yes," whispered Jack. He nodded over to Emily. "She doesn't know." "She thinks the baby died of SIDS."

"Why would you tell her that kind of lie?" demanded the Doctor.

Jack squared his shoulders and stared at the Doctor. "Her mother had just died. Our baby was dead, and she has no idea that a time lord was her father." Through clenched teeth, "why should I put her through more suffering than she has already experienced?"

"What about leaving her?" replied the Doctor coldly. "Didn't that cause suffering or was your marriage that bad?

Jack stood up, and it was only the restraining hand of Martha that kept him from going after the Doctor. "Don't talk about things you don't understand." Jack clenched his jaw, obviously wanting to say more, but deciding it was not the best time to do so. "I have a plan to protect Emily and get the Daleks out of here." He sat down heavily. "I've had it in mind for the last 5 years."

"What is it?" asked Martha while the Doctor silently glared at Jack.

Before Jack could answer, there was a loud bang at the door rapidly followed by more bangs and voices.

"What the . . ." began Jack, who looked at a startled Doctor and worried Martha. "Are you expecting anyone?"

"No," shouted Emily running past them, "I am."

_Present Time_

Donna had walked up and joined the others while they heard Emily obviously talking to a group of people. The Doctor had to admit that he had not heard her so excited since they first met. Martha, the Doctor and Jack looked at Donna.

"What is going on?" asked Martha.

Donna shrugged and looked amused. "She said that she was calling her backup team" She looked over at Jack. "Emily plans on going to Glastonbury."

"The source of the tear," said Jack. He got up and walked around. Then he stopped and stared at the group in horror. "Oh my God! I know what she plans to do." At that moment, Emily came running back in with her team which consisted of her three students, George, Frank, and Sherri.

"Guys," said Emily by way of introduction, "this is my team: George, Frank, and Sherri." The four had their arms slung around each other and were grinning. "We're going to Glastonbury to shut the tear and disarm the Daleks."

"You can't do that" snapped Jack. "You could all die."

"I don't understand" said Donna. "Why would they die?" "Isn't closing the tear a good thing?"

"Yes," said Emily looking at Jack for the first time. "It is a necessary choice."

"No!" shouted Jack, "It isn't."

"To close that tear," said the Doctor, "you would have to generate an incredible amount of energy." He looked at Emily. "You picked Glastonbury because of the magnetic energy there."

"Yes," she replied. "If I can control the energy there, I can bring everyone home and disarm the Daleks."

The Doctor raised his eyebrows. "How do you plan to control that energy?"

Emily looked at her team and smiled. George spoke up. "That is where our brilliance comes in." He looked over at Frank and Sherri. "Guys, if you will."

Sherri and Frank pulled out their Blackberry's and aimed them at each other. The result was a 3-D hologram of a machine. Emily pointed at the machine. "We created this machine to take the Earth's magnetic energy and use it to open an area in time and space." As she was speaking, the hologram was showing the machine from all sides. "Glastonbury is one of several spots around the world where magnetic energy is the strongest, but I picked it because the energy there is among the most ancient on Earth."

"With that type of energy," said Fred, picking up the lecture, "and our machine, we can transport people back and forth through time and close the tear."

"Furthermore," said Sherri, "we can use our own energy to take out the Daleks."

The Doctor felt his face drain. "You mean to hook yourself up to the machine, don't you?"

"No," said Emily, "I mean to hook myself up to the machine." She looked at the Doctor. "I've always been able to use my energy with the machine to bend space-time." "When I was in the Tardis, on our way here, I transmitted my energy through my phone to the machine. That's how people were taken to another universe."

"I take it those aren't regular Blackberry's," said Donna.

"Nope," said George, "One of my own design." "I've actually patent it . . ."

"You can't do that," said the Doctor tersely cutting him off. "The combination of that ancient energy and your DNA could kill you."

"It's what has to be done," said Emily, looking over at Jack. "You know that I am right."

"Emily," began Donna, "are you sure there is no other way?"

Emily looked at her new friend and smiled sadly. "I know if the Daleks find me that they will use me to create some sort of hybrid." She looked over at the Doctor. "I figured that out when we were on our way to London." She bit her lip and then looked at Jack. "I know that is why our baby died." Jack opened his mouth, but nothing came out. Emily walked over to her team and they linked arms. "I have to do this." She smiled. "I love you all." Then using their Blackberry's, Emily and her team disappeared.

"Emily!" shouted Jack as she faded away. He reached for her but she was gone. Sighing, he turned to the group with a grin escaping his face.

"You've got to hand it to her," he said to the Doctor, "she's got style."

"Emily's not the only one with a teleport machine," said Martha, "We can use it to get to Glastonbury."

The Doctor looked at Jack. "What's this five year plan of yours?"

"We don't have much time," said Jack breaking into a run with Martha alongside, "I'll explain along the way."

"Oh God!" exclaimed Donna, "Not more running."

"Come on," said the Doctor, "It's all part of the fun."

As they broke into a run, Donna told the Doctor. "I'm getting one of those phones from George, so I can teleport anywhere I want."

His laughter followed them down the hallway.


	10. Chapter 10

_Thor Hill_

_Glastonbury, England_

_2:30 p.m._

Emily and her team immediately began setting up the machine to open the portal to a parallel universe. Teams of Daleks roamed the city looking for humans destroy, and Emily knew that it was only a matter of time before the Daleks discovered that all humans were moved to a parallel universe. Emily felt that fortune was on her side since the Daleks had not discovered the machine. While George calibrated, Sherri and Frank began navigating the energy fields finding the lines where the ancient energy was strongest. Emily took a deep breath and began hooking herself up to the machine.

"Hey," said Sherri softly as she came over to help Emily, "your ex is right; you could die doing this."

Emily smiled and touched Sherri's cheek. "I've been dead a long time." She sighed and inserted the last coupling to her body. "I thought finding my father would help, but not even that has made a difference." She breathed in the cool afternoon air and smiled at Emily. "I need to do this." Sherri nodded and squeezed Emily's hand. Stepping back, Sherri joined Frank and George who were waiting by the prepped machine.

"Ready, when you are boss," said George.

Emily smiled and nodded. "You know what to do?"

"Yes," said Frank, "we're ready."

"Let's do it" said Emily.

Together, Frank, Sherri and George threw the main switches. Emily's body lit up and glowed gold.

_Meanwhile_

The Doctor, Donna, Jack and Martha arrived at another end of town as a burst of energy tore through the sky from Thor Hill. Donna gasped as Daleks took to the sky and headed toward Thor Hill. She turned to Jack. "Is your plan going to work?" He grinned. "I knew my wife well enough, so yes, I think the plan will work."

"You'd better hope so," said the Doctor.

Jack rolled his eyes. "You're not the only person who wants her safe."

The Doctor continued to glare at Jack, but motioned to Donna and Martha with a nod of his head. While Jack spoke into his Blackberry, the Doctor consulted with Donna and Martha.

"Did you bring it?" the Doctor asked Martha.

Martha tapped her pocket. "Yes, Doctor." She looked at him seriously. "Are you sure?"

The Doctor looked grim and pointed to the sky. "She is using all of her energy to open that tear." He nodded, "I just found her; I'm not going to lose her now." He held out his hand to Martha. "Give me the syringe."

For a moment, Martha hesitated, then reached into her pocket and handed it over. The Doctor took it, flicked his finger to check it, and then satisfied, he tucked it in his pocket. "Come on," he said to Donna and Martha, "we need to rejoin Jack." He and Martha started off, but the Doctor was stopped by Donna's hand. "Doctor, I need a word."

The Doctor stopped and turned to stare at her. "Donna, we don't have time for this."

Donna crossed her arms and glared at the Doctor. He sighed. Despite the chaos around them, he knew that if he did not stop and hear Donna out; she would make his life even more difficult. Swallowing his pride, he walked over and hung his shoulders. Seeing that she had him beaten, Donna gently grabbed the Doctor's hand and held it.

"Look," she began, "we did not travel together for a long time, but I feel I know you well enough." She cocked her head and smiled at him. "I know how badly you need a companion. Someone who won't die. Someone who will live with you forever . . ."

A sudden explosion turned their attention toward Thor Hill. Emily attached to the machine had opened the tear and ships came through the tear and began firing under Jack's command. In the last five years, Jack had been coordinating with the armed services concerning all possible scenarios, and like George, he had been working with Blackberry to create a phone service that could work in parallel worlds. Jack, as he told them during the teleport, was counting on his wife to create a machine and then use her power to program it. "I known since she was a baby that she had that power," said Jack, "Emily figured it out when she went to Harvard, and she's fought hard to deny it."

"Why?" asked Donna. "Why would she want to deny that power?"

"She didn't know how to control it," said Jack, "and without someone to guide it, she found that power frightening and isolating." He sighed. "After the baby died, she threw herself into her work and found a use for her power." He looked at the Doctor. "Emily doesn't care if she lives or dies." He shook his head. "You need to convince her otherwise."

The Doctor looked grimly at Donna, but said nothing. Turning his attention to Jack, he asked, "Now what?"

"Now," said Jack, "We go and meet the army."

While chaos flew overhead, Donna, the Doctor, Jack and Martha ran toward Thor Hill.

_Thor Hill_

George, Sherri and Frank managed to close the tear behind the army. George and Sherri managed to detach Emily from the machine and with Frank carrying Emily, the four of them ran down the hillside for cover. Halfway down, they were met by three Daleks. Sherri and George pointed their Blackberry's and fired. Two Daleks were destroyed, but the third Dalek managed to deflect the fired rays and the machine moved forward. It was soon joined by two other Daleks. Sherri and George fired again, but their rays were deflected. The Daleks had apparently been carefully planning for this time too. One Dalek rolled toward Frank and extended its arms.

"Give us the woman" it demanded. "She is a time lord."

"No!" shouted Frank. "You can't take her."

"You have no choice in this!" shouted the Dalek in return. All three Daleks opened fire.

"No!" shouted a voice that appeared to be running.

Frank, Sherri and George all collapsed as they were fired upon. One of the Daleks rolled up and tried to pick up Emily, but suddenly its circuitry went haywire. The other two Daleks rolled around and saw the Doctor running up with Jack, Donna and Martha.

"The Doctor!" shouted one of the Daleks. "Our greatest enemy!"

The Daleks were getting ready to open fire when a British air ship flew overhead. Using a focused laser, it destroyed the two Daleks. With a sweep of the area, the hovering Daleks beat a retreat into space. While Jack and the Doctor checked Emily, Martha and Donna checked Frank, Sherri and George. Martha and Donna looked at each other sadly. Emily's team, her three closest friends and students, were dead. Walking over, Martha and Donna sat with Jack and the Doctor to check on Emily. The energy from her body was dissipating. The Doctor looked at his three companions. "She's dying." He reached into his coat pocket and grabbed the syringe. Feeling on Emily's neck for her carotid artery, the Doctor poised it and was about to put it in when Jack grabbed his arm.

"What is that?" he asked.

"Recombined DNA." he replied. "My DNA combined with her existing DNA will make her . . ."

"Like you" replied Jack heavily. He looked at the Doctor for a moment, then released his arm.

"Doctor" began Donna.

"Donna," he snapped, "this has to be done or she will die!"

"It know," she said softly, "but it's wrong." She looked over at Martha. "Back me up here."

Martha stared directly at the Doctor as she spoke. "The Doctor is doing what he feels is best."

With that, the Doctor pushed the needle into Emily's artery. Using his thumb, he pushed the plunger and the recombined DNA into her body. Taking the needle out, the Doctor put his palm on her neck and waited. Emily's body continued to dissipate energy and grow colder, but nothing appeared to be happening. Suddenly, Emily's body convulsed and the last bit of energy disappeared. The Doctor who still had his hand on her neck felt her pulse die. He sat back and looked over at Jack.

"She's gone" he said.

Jack pulled Emily's body into his lap and held her while he cried. Donna looked questioningly at Martha who gestured for her friend to come over. They walked off a little ways down the hill. Meanwhile, teams of army officers came up to the party while British air ships continued to drive the Daleks back into space.

_Uffington, England_

_3 days later_

The Doctor and Jack led the funeral procession up the hill. Jack held an urn while the Doctor strolled quietly along side him. They were followed by Martha, Donna and several of Emily's colleagues and friends. Upon reaching the top of the hill, the group gathered. Friends and colleagues shared remembrances, while Jack sang one of Emily's favorite songs. Donna and Martha both cried while the Doctor stood stone-faced. Jack turned and released Emily's ashes into the air. Then the group turned and headed down the hill. The Doctor stood still as if he were in a trance. Then he called to Martha.

"Martha," he called, "could we have a word?"

Martha turned and walked back up the hill. She and the Doctor stared at each other for a moment. Martha sighed and bit her lip. "You figured it out, didn't you?"

"There was nothing in that plunger was there?" said the Doctor.

"No," said Martha, "it was a placebo."

"Why?" he demanded angrily. "you knew how much I needed her."

"Exactly," responded Martha, "it is always about you." She crossed her arms and glared at him. "Did you ever stop to think about what she needed or wanted?" Martha cocked her head to one side. "Did you even think to ask?"

With his anger deflating, the Doctor stared at the ground. "There was no time."

"There never is with you," said Martha, "kind of ironic, really, since you are a time lord."

The Doctor stuffed his hands in his pockets and stared out over the hills. "I'm alone again."

Martha walked up to him and linked her arm through his. "Doctor, you are never alone." The two started down the hill together. "You have us even if we die and decay." "You will always have companions and they can learn so much from you." She smiled at him. "Maybe that is your purpose in life."

_Oxford, England_

The Doctor walked over to the Tardis and ran his fingers over the old wood. No matter how many people he lost in his life, the Tardis remained his one constant. Maybe, he thought, the Tardis is his true love. Unlocking the door, the inside sprung to life. Staring at the computer screen, the Doctor looked for the Face of Boe, but there was no one there. After the funeral, all of his companions left: Jack returned to Torchwood, Martha to the Unit and her fiancée, Donna to her company and new boyfriend. It seemed to the Doctor that everyone moved on while he remained static. Sure, he traveled the universe through time and space, but that was all he ever did.

Well, he thought, there was no point in feeling sorry for himself.

The Doctor went to the controls when suddenly there was a rift that tore through the Tardis. A human form descended and landed inside the Tardis. Immediately, the Doctor ran over and turned her over. From there, he stumbled back in shock. It was Emily. She was dressed in military fatigues. Behind her in the rift, he could see a battle. Running over to the controls, he pulled the Tardis back and ran back to Emily. She looked him as though he was a stranger.

"Who are you?" she demanded.

"I'm the Doctor" he said breathlessly. "And you?"

"Lt. Emily Smith, second commander of the 455th battalion," she said breathlessly as she stood up.

"What battle?" he asked.

She looked at him strangely. "World War Three in 2125." She looked around the box. "How do I get out of here?"

The Doctor pointed to the door. "That way."

Emily started out the door and then stopped. "You're a doctor?" He nodded. "Are you up to an adventure, because I could use your help."

"Yes," said the Doctor grinning. "I'd love to help."

"Just so you know" said Emily as she opened the door to the sounds of battle. "there is an awful lot of running to do."

The Doctor just grinned. "I wouldn't have it any other way."


End file.
